tbuckley/cabot-search huggingface dataset:
Accurate Identification of Subclones in Tumor Genomes
Authors: Navid Ahmadinejad, Shayna Troftgruben, Junwen Wang, Pramod B Chandrashekar, Valentin Dinu, Carlo Maley, Li Liu
Journal: Molecular Biology and Evolution (2022)

Understanding intratumor heterogeneity is critical for studying tumorigenesis and designing personalized treatments. To decompose the mixed cell population in a tumor, subclones are inferred computationally based on variant allele frequency (VAF) from bulk sequencing data. In this study, we showed that sequencing depth, mean VAF, and variance of VAF of a subclone are confounded. Without considering this effect, current methods require deep-sequencing data (>300× depth) to reliably infer subclones. Here, we present a novel algorithm that incorporates depth-variance and mean-variance dependencies in a clustering error model and successfully identifies subclones in tumors sequenced at depths of as low as 30×. We implemented the algorithm as a model-based adaptive grouping of subclones (MAGOS) method. Analyses of computer simulated data and empirical sequencing data showed that MAGOS outperformed existing methods on minimum sequencing depth, decomposition accuracy, and computation efficiency. The most prominent improvements were observed in analyzing tumors sequenced at depths between 30× and 200×, whereas the performance was comparable between MAGOS and existing methods on deeply sequenced tumors. MAGOS supports analysis of single-nucleotide variants and copy number variants from a single sample or multiple samples of a tumor. We applied MAGOS to whole-exome data of late-stage liver cancers and discovered that high subclone count in a tumor was a significant risk factor of poor prognosis. Lastly, our analysis suggested that sequencing multiple samples of the same tumor at standard depth is more cost-effective and robust for subclone characterization than deep sequencing a single sample. MAGOS is available at github (https://github.com/liliulab/magos).
PB1862: BRUIN CLL-313: A PHASE 3 OPEN-LABEL, RANDOMIZED STUDY OF PIRTOBRUTINIB VS BENDAMUSTINE+RITUXIMAB IN UNTREATED PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA/SMALL LYMPHOCYTIC LYMPHOMA (TRIAL IN PROGRESS)
Authors: W. Jurczak, C. Dartigeas, M. Coscia, P. Ganly, G. Al-Jazayrly, C. Wang, K. Bao, C. C. Leow, S. Shahda, P. L. Zinzani
Journal: HemaSphere (2022)

Background: Covalent Bruton's Tyrosine Kinase (BTK) inhibitors (BTKi) have transformed the management of chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), but these treatments are not curative and the majority of patients will require additional treatment. Covalent BTKi share pharmacologic liabilities (e.g. low oral bioavailability, short half-life) that collectively may lead to suboptimal BTK target coverage, for example in rapidly proliferating tumors with high BTK protein turnover such as accelerating CLL/SLL, ultimately manifesting as acquired resistance in some patients. Aims: To address these limitations, pirtobrutinib, a highly selective, non-covalent BTKi that inhibits both wild type (WT) and C481-mutated BTK with equal low nM potency was developed. In a phase 1/2 BRUIN study, pirtobrutinib achieved pharmacokinetic exposures that exceeded its BTK IC96 at trough, was well tolerated, and demonstrated promising efficacy in CLL/SLL patients regardless of prior therapy, number of prior lines of therapy, or BTK C481 mutation status. Methods: BRUIN CLL-313 is a randomized, open-label, global phase 3 study comparing pirtobrutinib monotherapy versus bendamustine plus rituximab (BR) in treatment naïve CLL/SLL patients with retained 17p. Approximately 250 patients will be randomized 1:1. Randomization will be stratified by IGHV mutation status (mutated vs unmutated), and Rai stage (low/intermediate vs high). Patients in the BR arm are eligible to crossover to pirtobrutinib monotherapy if they experience progressive disease per iwCLL 2018 and confirmed by an independent review committee (IRC). Eligible patients are adults with confirmed diagnosis of CLL/SLL and who require therapy per iwCLL 2018 criteria. Key exclusion criteria include CNS involvement by CLL/SLL, Richter transformation to DLBCL, prolymphocytic leukemia or Hodgkin lymphoma any time pre-enrollment, presence of 17p deletion, prior systemic therapy for CLL/SLL, and significant cardiovascular disease. The primary endpoint is progression-free survival (PFS) per iwCLL assessed by an independent review committee. Secondary endpoints include investigator-assessed PFS, overall survival (OS), overall response rate (ORR), duration of response (DoR), safety and tolerability, and patient reported outcomes. The global study is currently enrolling patients. Results: This study is a Trial in Progress. The results will be presented at a later date. Summary/Conclusion: This study is a Trial in Progress. The conclusions will be presented at a later date.
S105: IN VIVO PDX CRISPR/CAS9 SCREENS REVEAL MUTUAL THERAPEUTIC TARGETS TO OVERCOME HETEROGENEOUS ACQUIRED CHEMO-RESISTANCE
Authors: A.-K. Wirth, L. Wange, S. Vosberg, A. K. Jayavelu, W Enard, T Herold, I Jeremias
Journal: HemaSphere (2022)

Background: Acquired resistance to conventional polychemotherapy regimens leads to relapse and poor prognosis, and remains a major unmet clinical need. Aims: To identify therapeutic options to overcome acquired chemo-resistance. Methods: We studied acute lymphoblastic leukemia (ALL) as model disease and combined long-term in vivo treatment in orthotopic patient-derived xenograft (PDX) models with multi-omics profiling and functional genomic CRISPR/Cas9 screens. Results: We adapted conventional chemotherapeutic protocols to allow treatment of mice for up to 18 consecutive weeks, using a combination of the widely used drugs cyclophosphamide and vincristine. Three luciferase-transgenic PDX models were monitored by repetitive in vivo imaging. Polychemotherapy strongly reduced PDX ALL cells within the first weeks, proving initial sensitivity of the sample. Under continuous treatment, tumor load persisted in mice at the level of minimal residual disease for several weeks, until tumors resumed growth despite treatment, indicating acquired resistance. In an exemplary PDX model, eight resistant derivatives were generated in replicate mice and characterized individually. Genomic profiling revealed profound genomic heterogeneity between distinct derivatives; individual resistant derivatives acquired different copy number alterations in regions associated with resistance and distinct point mutations, e.g. in TP53. In contrast to genomic heterogeneity, transcriptome and proteome profiling identified a group of genes differentially expressed between sensitive and resistant cells, but similar across all derivatives. To gain insights into underlying mechanisms and to identify therapeutic targets to overcome acquired resistance, a customized CRISPR/Cas9 in vivo dropout screen was performed in individual resistant PDX derivatives, to test the relevance of around 200 candidate genes under treatment. Among others, sgRNAs targeting BCL2, BRIP1 or COPS2 dropped out in the in vivo screen specifically during treatment; single knockout experiments confirmed that knockout of either BCL2, BRIP1 or COPS2 re-sensitized PDX ALL cells towards chemotherapy. Of direct translational relevance, treatment of mice with the BCL2 inhibitor ABT-199 sensitized resistant PDX cells towards polychemotherapy in vivo. Interestingly, BCL2 inhibition restored treatment response in resistant derivatives independently from the highly diverse underlying genetic alterations, e.g., in clones with and without mutation in TP53. Summary/Conclusion: Taken together, we established a highly clinically relevant PDX in vivo model of acquired resistance to conventional chemotherapy. Using this model, we demonstrate that heterogeneous genomic alterations evolved in parallel in replicate mice, which could be overcome by a single therapeutic approach to re-sensitize tumors towards conventional chemotherapy.
PB1823: SECONDARY ACUTE MYELOID LEUKEMIA AND DE NOVO ACUTE MYELOID LEUKEMIA WITH MYELODYSPLASIA-RELATED CHANGES DISTINCT LANDSCAPE, OR THE SAME DISEASE?
Authors: M. Jagurinoski, E. Aleksov, M. Stojcov-Jagurinoska, I. Tonev, R. Vladimirova, Y. Davidkova, G. Balatzenko, B. Spassov, M. Guenova
Journal: HemaSphere (2022)

Background: Acute myeloid leukemia (AML) with myelodysplasia-related changes is a heterogeneous category in the WHO classification. It includes both AML occurring de novo which harbors myelodysplastic morphological and/or cytogenetic features (dn-AML-MDS), and “secondary” AMLs after a previous myeloid neoplasm, e.g., myelodysplastic syndrome (MDS) or myeloproliferative neoplasms or aplastic anemia (s-AML-MDS). There is still uncertainty about the affiliation of these categories to a common pathogenetic and clinical course. Aims: To perform a comparative analysis between patients with AML secondary to MDS and dn-AML-MDS. Methods: A total of 63 patients (58.7% men and 41.3% women), mean age 62 years (range, 21-85 years), divided into two groups, s-AML-MDS (n=30) and dn-AML-MDS (n=33), were analyzed. Diagnosis was based according to WHO classification criteria (2016). Results: Comparative analysis showed no differences in demographic characteristics, hematologic parameters, and % of blasts in bone marrow or peripheral blood between the groups. Morphological analysis revealed dysplasia in more than one cell lineage in all patients, with significantly higher incidence of granulocytic dysplasia in the dn-AML-MDS 30/32 (93.8%) vs. s-AML-MDS 16/27 (59.3%) (p<0.001). The phenotypic profile showed no differences between the groups, either in terms of early markers CD34, CD117 or aberrant expression of lymphoid markers. We observed a higher incidence of aberrant karyotypes in dn-AML-MDS vs. s-AML-MDS (71.4% vs. 40%, p=0.02). Patients with dn-AML-MDS had a higher frequency of abnormalities on chromosome 7 and chromosome X in contrast to s-AML-MDS (respectively, 32.1% and 21.4% vs. 8% and 0.0%, p=0.031 and р=0.014). Molecular analysis also showed differences, as the FLT3-ITD mutation, was observed in only one case (4.2%) with dn-AML-MDS while in 30% with s-AML-MDS, respectively (p=0.02). No differences were found with respect to mutations in the NPM1 gene and EVI1 overexpression. During the follow-up period, s-AML-MDS showed a 13.8% survival rate compared to 33.3% in dn-AML-MDS patients, and the median survival in both groups was very short, 5.9 mo. (SE 0.85, p>0.05). Summary/Conclusion: AML-MDS occurring de novo or as a “secondary” disease unites categories with extremely unfavorable prognosis that show similarities but also differences in biological features. The accumulation of knowledge in the field of genomic, epigenetic changes determining its course, could lead to the construction of new algorithms for more accurate diagnosis, risk assessment and personalized therapeutic approach.
Vascularized Lung Cancer Model for Evaluating the Promoted Transport of Anticancer Drugs and Immune Cells in an Engineered Tumor Microenvironment (Adv. Healthcare Mater. 12/2022)
Authors: Dasom Kim, Kyeong Seob Hwang, Eun U Seo, Suyeong Seo, Byung Chul Lee, Nakwon Choi, Jonghoon Choi, Hong Nam Kim
Journal: Advanced Healthcare Materials (2022)
P1579: PHOTOBIOMODULATION FOR CHEMOTHERAPY-INDUCED ORAL MUCOSITIS IN LEUKEMIC CHILDREN: A RANDOMIZED CONTROLLED CLINICAL TRIAL
Authors: Y. El Chazli, F. Reyad, N. Elsayed
Journal: HemaSphere (2022)

Background: Oral mucositis (OM) comes on the top of the most serious and frequent complications in children with cancer, with incidence rates ranging from 52% to 100% of patients receiving high-dose CT. Rapid cellular mitosis makes children more susceptible to CT and hence to OM than adults. Another risk factor for OM in leukemic children is the associated neutropenia. Low-level laser therapy (LLLT) or “Photobio-modulating (PBM) lasers is a therapeutic modality having three main effects: reducing inflammation and edema, promoting wound healing, and treating pain. Aims: Evaluation of the effectiveness of low-level laser treatment (LLLT) for chemotherapy-induced oral mucositis in children suffering from acute leukemia. Methods: A randomized controlled clinical study including forty-four leukemic children diagnosed with chemotherapy-induced OM at the Hematology/Oncology inpatient unit at Alexandria University Children’s Hospital, Alexandria, Egypt. Patients were randomly assigned to either the control or test groups with a 1:1 ratio. The control group received conventional symptomatic treatment, while the test group was treated with LLLT in addition to the symptomatic treatment. The response to both treatment modalities was evaluated according to the reduction of pain and lesions severity from baseline to 5, 10, and 14 days after treatment. Results: The patients’ age ranged from 4 to 11 years. They were all diagnosed with ALL, 79.5% had B-ALL, and 20.5% had T-ALL. They were all treated according to the Total XV study protocol. A significant reduction of pain was recorded on day 10 in the test group compared to the control group (p <0.001). Furthermore, there was a significant decline in the mean VAS among the test group starting from day5. There was also a significant decline in the OM grades between the two groups on day14 (p = 0.003). No adverse events were reported. Summary/Conclusion: The use of LLLT along with the conventional treatment was effective in reducing pain and in the recovery of OM lesions in children receiving chemotherapy for the treatment of ALL. It was also safe and applicable to children.
PB2072: EFFICACY AND SIDE EFFECTS OF IBRUTINIB IN RELAPSED AND REFRACTORY MANTLE CELL LYMPHOMA
Authors: A. Basturk, M. Bagci, M. S. Dal, T. Hacibekiroglu, S. Kabukcu Hacioglu, I. Aydogdu, M. Kizil Cakar, C. Sunu, G. Akgun Cagliyan, A. Kaya, M. H. Dogu, S. Celik, H. Uskudar Teke, M. A. Erkurt, O. Ekinci, B. Turgut, A. Tekinalp, S. Korkmaz, T. Ulas, F. Altuntas
Journal: HemaSphere (2022)

Background: Mantle cell lymphoma constitutes 6–8% of all B-cell lymphomas. Due to its efficacy and reliability, ibrutinib has been used to treat patients with mantle cell lymphoma who experience a relapse after transplantation, similar to patients with other B-cell malignancies. Aims: The purpose of the present study was to evaluate the efficacy and side effects of ibrutinib in patients with relapsed and refractory mantle cell lymphoma. Methods: This retrospective study included 37 patients with relapse/refractory mantle cell lymphoma who were over the age of 18 years and who were treated in 16 different healthcare centers. The patients’ responsiveness to the administration of ibrutinib, the duration of the response, the prognostic factors affecting the response, and the side effects associated with ibrutinib were analyzed retrospectively. Results: The median follow-up period was eight months. The total response rate was 58% (19.3%, CR). The mean life expectancy was 31.3 months. The mean period to achieve complete remission was four months. While 51.6% of patients responded three months after the initiation of ibrutinib treatment, this rate increased to 56.5% at six months, and to 66.7% at 12 months. In 40.5% of the patients, the duration of treatment was longer than 12 months, and in 13.5% of the patients, it was longer than 24 months. Summary/Conclusion: Our study confirmed the findings of previous studies that the use of ibrutinib in the treatment of R/R MCL was effective and reliable.
PB1808: LANGERHANS CELL HISTIOCYTOSIS IN ADOLESCENT PATIENTS: A SINGLE-CENTER RETROSPECTIVE STUDY
Authors: H. Cai, J. Chen, T. Liu, H. Cai, M. Duan, J. Li, D. Zhou, X. Cao
Journal: HemaSphere (2022)

Background: Langerhans cell histiocytosis (LCH) is a myeloid dendritic cell disorder frequently affecting children and adults, however the clinical characteristics and genetic profiles of adolescent LCH remain elusive. Aims: This research focused on the clinical and genetic features of adolescent LCH and aimed to address the knowledge gap. Methods: We performed a single-center retrospective study of 36 adolescent LCH patients aged between 14 and 17 years. Results: At the time of diagnosis, 10 patients were classified as unifocal single system LCH (27.8%), 2 patients had pulmonary single system LCH (5.6%), 5 patients had multifocal single system LCH with bone involvement (13.9%), and 19 patients had multisystem LCH (52.8%). The most prevalent involvement in multisystem patients was pituitary gland (78.9%), followed by the bone (42.1%), lung (42.1%), and lymph nodes (42.1%). Eight (42.1%) patients had risk organ involvement. BRAFN486_P490 was detected in 50% of patients who underwent next generation sequencing. One patient died and thirteen patients relapsed during the follow up. The estimated 5-year OS rate and EFS rate were 94.7% and 59.0%, respectively. Adolescent patients resembled previously reported adult LCH series in organ involvements, prevalent BRAF deletion mutations and clinical outcomes. Summary/Conclusion: As the largest adolescent LCH cohort to date, our study found that the clinical characteristics of adolescent LCH patients may be close to adult LCH.
PB2294: CHEMOTHERAPY INDUCED THROMBOCYTOPENIA AND ITS ASSOCITAION WITH COAGULOPATHY; A SINGLE CENTRE EXPERIENCE
Authors: N. ANWAR, N. FATIMA, A. KHALID, L. MAJEED, M. BORHANY
Journal: HemaSphere (2022)

Background: Chemotherapy induced thrombocytopenia is perilous and may complicate disease treatment resulting in extended hospitalisation, bleeding, platelet transfusion and increase economic burden on the patients. Typically patients with hematological malignancies are at high risk of thrombosis and hemorrhage which may lead to poor outcome and overall survival. As coagulopathy in hematological malignancies is a predictor of thrombotic and bleeding complications, by adding the intellectual observation of platelet count, we may segregate patients and identify the susceptibility to either thrombosis or bleeding apparently. Our center is a referral institute for management of blood disorders with huge representation of patients with hematological malignancies. Aims: The study was done to observe the association of chemotherapy induced thrombocytopenia with coagulopathy in patients with hematological malignancies. Methods: This was a retrospective cohort study done at NIBD PECHS campus from 2020-2021. All the patients diagnosed with hematological malignancies receiving chemotherapy during the study period were included. Patients who had thrombocytopenia before chemotherapy were excluded. PT, APTT and platelet count, post chemotherapy was assessed. Chi square test and Fisher exact test was applied to observe the association. P-value <0.05 was considered to be statistically significant. Results: A total of 34 chemotherapy cycles for hematological malignancies were analyzed. Median and range of age of patients was 36(9-75years) with predominant representation of male patients. Median platelet count post chemo was 39x109/L (4-398). The overall incidence of chemotherapy induced thrombocytopenia was 18%. Overall PT and APTT were deranged in 21(61.8%) and 24(70.6%) cases respectively. The association between chemotherapy induced thrombocytopenia and PT and APTT was observed however it was found out that deranged PT and APTT results were not associated with thrombocytopenia and found to be statistically non-significant (P-value >0.05). Summary/Conclusion: In conclusion, the association of chemotherapy induced thrombocytopenia with coagulopathy was not found statistically significant. However, the findings might suggest the identification of high risk cohort at risk of bleeding and/or thrombosis. Longitudinal studies with larger sample size are needed in this regard.
Lipid nanoparticle-mediated silencing of osteogenic suppressor GNAS leads to osteogenic differentiation of mesenchymal stem cells in vivo
Authors: Genc Basha, Andrew G. Cottle, Thavaneetharajah Pretheeban, Karen YT. Chan, Dominik Witzigmann, Robert N. Young, Fabio MV. Rossi, Pieter R. Cullis
Journal: Molecular Therapy (2022)

Approved drugs for the treatment of osteoporosis can prevent further bone loss but do not stimulate bone formation. Approaches that improve bone density in metabolic diseases are needed. Therapies that take advantage of the ability of mesenchymal stem cells (MSCs) to differentiate into various osteogenic lineages to treat bone disorders are of particular interest. Here we examine the ability of small interfering RNA (siRNA) to enhance osteoblast differentiation and bone formation by silencing the negative suppressor gene GNAS in bone MSCs. Using clinically validated lipid nanoparticle (LNP) siRNA delivery systems, we show that silencing the suppressor gene GNAS in vitro in MSCs leads to molecular and phenotypic changes similar to those seen in osteoblasts. Further, we demonstrate that these LNP-siRNAs can transfect a large proportion of mice MSCs in the compact bone following intravenous injection. Transfection of MSCs in various animal models led to silencing of GNAS and enhanced differentiation of MSCs into osteoblasts. These data demonstrate the potential for LNP delivery of siRNA to enhance the differentiation of MSCs into osteoblasts, and suggests that they are a promising approach for the treatment of osteoporosis and other bone diseases.